Our earlier work has used a variety of cell-based and in vitro systems to explore the role of mitochondria in apoptosis. In particular, previous studies have shown that Bcl-2-family proteins can act directly on liposomal membranes to make them permeable to large macromolecules. Whereas this very simple system, using defined liposomes and mixtures of recombinant Bcl-2-family proteins has proven to be useful for defining the functions of these proteins in the absence of other proteins, the situation in the native mitochondrion is of course much more complex. Here we describe experiments designed to test hypotheses concerning 1) protease regulation of mitochondrial outer membrane permeabilization (MOMP), 2) cellular consequences of MOMP in the absence of active caspases, and 3) the regulation of mitochondrial apoptosis pathways in vivo, in Xenopus development.